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Coexpression cluster:C4238: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!1.78e-30!115;UBERON:0000025!3.21e-26!194;UBERON:0001049!1.47e-23!57;UBERON:0005068!1.47e-23!57;UBERON:0006241!1.47e-23!57;UBERON:0007135!1.47e-23!57;UBERON:0004111!2.22e-22!241;UBERON:0003075!8.70e-22!86;UBERON:0007284!8.70e-22!86;UBERON:0000477!1.05e-19!286;UBERON:0000955!1.11e-19!69;UBERON:0006238!1.11e-19!69;UBERON:0000483!1.92e-19!309;UBERON:0002346!2.73e-19!90;UBERON:0005743!4.12e-19!86;UBERON:0002616!5.44e-19!59;UBERON:0000119!1.42e-18!312;UBERON:0001017!3.89e-18!82;UBERON:0003080!6.53e-18!42;UBERON:0000073!1.67e-17!94;UBERON:0001016!1.67e-17!94;UBERON:0000475!2.25e-17!365;UBERON:0002780!2.71e-17!41;UBERON:0001890!2.71e-17!41;UBERON:0006240!2.71e-17!41;UBERON:0001893!4.52e-16!34;UBERON:0002020!6.81e-16!34;UBERON:0003528!6.81e-16!34;UBERON:0002791!2.10e-15!33;UBERON:0004872!2.27e-15!84;UBERON:0002619!5.07e-15!22;UBERON:0001981!5.12e-15!60;UBERON:0007500!5.12e-15!60;UBERON:0004537!5.12e-15!60;UBERON:0006965!5.12e-15!60;UBERON:0001869!5.62e-15!32;UBERON:0000468!9.82e-15!659;UBERON:0003056!1.48e-14!61;UBERON:0000055!4.18e-14!69;UBERON:0001950!7.84e-14!20;UBERON:0000481!6.05e-13!347;UBERON:0002049!3.08e-12!79;UBERON:0007798!3.08e-12!79;UBERON:0000956!9.64e-12!25;UBERON:0000203!9.64e-12!25;UBERON:0001637!8.66e-11!42;UBERON:0003509!8.66e-11!42;UBERON:0004572!8.66e-11!42;UBERON:0000467!2.96e-10!625;UBERON:0000153!4.16e-10!129;UBERON:0007811!4.16e-10!129;UBERON:0000480!4.45e-10!626;UBERON:0000033!4.63e-10!123;UBERON:0000064!1.72e-09!219;UBERON:0001009!2.22e-09!113;UBERON:0004535!1.45e-08!110;UBERON:0004573!1.98e-08!33;UBERON:0004571!1.98e-08!33;UBERON:0003914!3.57e-08!118;UBERON:0004121!4.12e-08!169;UBERON:0000924!3.03e-07!173;UBERON:0006601!3.03e-07!173;UBERON:0000947!6.38e-07!21;UBERON:0010191!6.38e-07!21;UBERON:0002050!7.16e-07!605;UBERON:0005423!7.16e-07!605;UBERON:0003076!7.28e-07!15;UBERON:0003057!7.28e-07!15
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0.205954,0.0750181
}}
}}

Revision as of 12:36, 5 September 2012


Full id: C4238_brain_nonsmall_spinal_Olfactory_insula_frontal_temporal



Phase1 CAGE Peaks

Hg19::chr2:56410948..56411039,+p2@CCDC85A
Hg19::chr2:56411109..56411130,+p4@CCDC85A
Hg19::chr2:56411131..56411187,+p1@CCDC85A


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
mesodermal cell4.49e-10119
lining cell5.44e-0757
barrier cell5.44e-0757
Uber Anatomy
Ontology termp-valuen
adult organism1.78e-30115
tube3.21e-26194
neural tube1.47e-2357
neural rod1.47e-2357
future spinal cord1.47e-2357
neural keel1.47e-2357
anatomical conduit2.22e-22241
neural plate8.70e-2286
presumptive neural plate8.70e-2286
anatomical cluster1.05e-19286
brain1.11e-1969
future brain1.11e-1969
epithelium1.92e-19309
neurectoderm2.73e-1990
regional part of brain5.44e-1959
cell layer1.42e-18312
central nervous system3.89e-1882
anterior neural tube6.53e-1842
regional part of nervous system1.67e-1794
nervous system1.67e-1794
organism subdivision2.25e-17365
regional part of forebrain2.71e-1741
forebrain2.71e-1741
future forebrain2.71e-1741
telencephalon4.52e-1634
gray matter6.81e-1634
brain grey matter6.81e-1634
regional part of telencephalon2.10e-1533
splanchnic layer of lateral plate mesoderm2.27e-1584
regional part of cerebral cortex5.07e-1522
blood vessel5.12e-1560
epithelial tube open at both ends5.12e-1560
blood vasculature5.12e-1560
vascular cord5.12e-1560
cerebral hemisphere5.62e-1532
multi-cellular organism9.82e-15659
pre-chordal neural plate1.48e-1461
vessel4.18e-1469
neocortex7.84e-1420
multi-tissue structure6.05e-13347
vasculature3.08e-1279
vascular system3.08e-1279
cerebral cortex9.64e-1225
pallium9.64e-1225
artery8.66e-1142
arterial blood vessel8.66e-1142
arterial system8.66e-1142
anatomical system2.96e-10625
anterior region of body4.16e-10129
craniocervical region4.16e-10129
anatomical group4.45e-10626
head4.63e-10123
organ part1.72e-09219
circulatory system2.22e-09113
cardiovascular system1.45e-08110
systemic artery1.98e-0833
systemic arterial system1.98e-0833
epithelial tube3.57e-08118
ectoderm-derived structure4.12e-08169
ectoderm3.03e-07173
presumptive ectoderm3.03e-07173
aorta6.38e-0721
aortic system6.38e-0721
embryonic structure7.16e-07605
developing anatomical structure7.16e-07605
posterior neural tube7.28e-0715
chordal neural plate7.28e-0715


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.019052471480264
CTCF#1066435.360256373075030.0064925092527670.0280264186926401
HMGN3#932438.178547723350590.001827766942164210.0108924480269722
RAD21#5885310.35503389545630.0009004912073565420.00665862370469484
SMC3#9126315.04493284493280.0002935825420371870.00309805669473797
YY1#752834.911170749853860.008441455341808260.0330218426265306
ZNF143#7702313.50087655222790.0004062804962997170.00389888162758854
ZNF263#1012738.221841637010680.001799043925565870.0109691370507428



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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